repicc {ENmix} | R Documentation

## Calculating intraclass correlation coefficient using replicate samples

### Description

The function can be used to calculate ICC for each CpG probe using balanced or unbalanced replicate samples.

### Usage

    repicc(dat,repid,mvalue=FALSE,nCores=2,qcflag=FALSE,qc=NULL,
           detPthre=0.05,nbthre=3)

### Arguments

`dat` | Methylation beta value matrix
`repid` | A data frame with two variables, id and idx. id should be the same with column name of "dat", idx is a variable to show the relationship between samples with same value for samples from same individual.
`mvalue` | If TRUE, the beta value will be converted to M value for calculation of ICC
`nCores` | Number of cores will be used for calculation of ICC
`qcflag` | Whether to perform QC before calculation of ICC
`qc` | QC object from function QCinfo
`detPthre` | If qcflag=TRUE, the methylation values with detection P value higher than the threshold will be removed before calculation
`nbthre` | If qcflag=TRUE, the methylation values with number of bead smaller

### Value

A data frame containing ICC for each probe

### Author(s)

Zongli Xu

### References

Zongli Xu, Jack A Taylor. Reliability of DNA methylation measures using Illumina methylation BeadChip. Epigenetics 2020

### Examples

    if (require(minfiData)){
    path <- file.path(find.package("minfiData"),"extdata")
    rgSet <- readidat(path = path,recursive = TRUE)
    mdat=getmeth(rgSet)
    beta=getB(mdat,"Illumina")
    repid=data.frame(id=c("5723646052_R02C02","5723646052_R04C01","5723646052_R05C02","5723646053_R04C02","5723646053_R05C02","5723646053_R06C02"),idx=c(1,2,3,1,2,3))
    iccresu<-repicc(dat=beta,repid=repid)
    }

[Package ENmix version 1.30.03 Index]